Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
081cde4c
Commit
081cde4c
authored
Jun 10, 2014
by
Peter van 't Hof
Browse files
example jsons changed/added
parent
c8269286
Changes
4
Hide whitespace changes
Inline
Side-by-side
flexiprep/nbactions.xml
View file @
081cde4c
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1
../
input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1
../
input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1
../
input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
gatk/examples/test.json
View file @
081cde4c
{
"inputtype"
:
"rna"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"bwa"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"flexiprep"
:
{
...
...
mapping/examples/test.json
0 → 100644
View file @
081cde4c
{
"referenceFile"
:
"/blabla/blabla.fa"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"flexiprep"
:
{
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"cutadapt"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"sickle"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
}
}
}
mapping/nbactions.xml
View file @
081cde4c
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment